Purpose <p>Edible swiftlet’s nest (ESN) is a prized delicacy harvested from swiftlet nests, often contaminated with inedible materials such as feathers, dust, and woody fragments. The cleaning process is labor-intensive due to sticky glycoproteins binding these impurities. While cleaned ESN is highly valued, the by-product (ESN-BP), which still contains glycoproteins and other materials, is typically discarded.</p> Methods <p>This study explores an eco-friendly biotechnology approach to recover valuable glycoproteins from ESN by-products through enzymatic hydrolysis, solubilizing the edible components into bioactive glycopeptide hydrolysate. This method enables the separation of edible material from inedible residues like bird feathers while enhancing nutritional properties. The study analyses the physicochemical properties, bioactivities (particularly antioxidative activity), molecular structure, and toxicity of the glycopeptide recovered from ESN-BP.</p> Results <p>Results show that the physicochemical properties of ESN-BP are similar to cleaned ESN, with enzymatic hydrolysis breaking down glycoproteins into soluble glycopeptides and free peptides. The molecular weight distribution of hydrolysates from ESN-BP exhibited a wider peptide fraction range compared to cleaned ESN. Antioxidative activity was comparable in both hydrolysates. Although slight toxicity was observed in the by-product hydrolysates, the study recommends using eco-friendly, chemical-free cleaning methods to recover glycoproteins, providing a cost-effective alternative for consumers.</p> Conclusion <p>Enzymatic hydrolysis enables the safe and cost-effective valorization of edible swiftlet’s nest by-products into bioactive functional food ingredients with enhanced nutritional functionalities and broader industrial utilization.</p> Graphical Abstract <p></p>